Integration nominal variable result

api/src/engine/connectors/datashield/datashield.connector.ts

@@ -8,17 +8,20 @@ import {
 } from 'src/common/interfaces/utilities.interface';
 import { errorAxiosHandler } from 'src/common/utils/shared.utils';
 import { ENGINE_MODULE_OPTIONS } from 'src/engine/engine.constants';
+import EngineService from 'src/engine/engine.service';
 import ConnectorConfiguration from 'src/engine/interfaces/connector-configuration.interface';
 import Connector from 'src/engine/interfaces/connector.interface';
 import EngineOptions from 'src/engine/interfaces/engine-options.interface';
 import { Domain } from 'src/engine/models/domain.model';
 import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
+import { AllowedLink } from 'src/engine/models/experiment/algorithm/nominal-parameter.model';
 import { Experiment } from 'src/engine/models/experiment/experiment.model';
 import { RawResult } from 'src/engine/models/result/raw-result.model';
 import {
   TableResult,
   TableStyle,
 } from 'src/engine/models/result/table-result.model';
+import { Variable } from 'src/engine/models/variable.model';
 import { ExperimentCreateInput } from 'src/experiments/models/input/experiment-create.input';
 import { User } from 'src/users/models/user.model';
 import {
@@ -27,6 +30,8 @@ import {
   transformToDomain,
   transformToHisto,
   transformToTable,
+  transformToTableNominal,
+  transfoToHistoNominal as transformToHistoNominal,
 } from './transformations';
 
 export default class DataShieldConnector implements Connector {
@@ -35,6 +40,7 @@ export default class DataShieldConnector implements Connector {
   constructor(
     @Inject(ENGINE_MODULE_OPTIONS) private readonly options: EngineOptions,
     private readonly httpService: HttpService,
+    private readonly engineService: EngineService,
   ) {}
 
   getConfiguration(): ConnectorConfiguration {
@@ -77,17 +83,65 @@ export default class DataShieldConnector implements Connector {
   }
 
   async getAlgorithms(): Promise<Algorithm[]> {
-    return [];
+    return [
+      {
+        id: 'linear-regression',
+        label: 'Linear Regression',
+        description:
+          'Linear regression analysis is a method of statistical analysis that fits a linear function in order to predict the value of a covariate as a function of one or more variables. Linear regression is a simple model that is easy to understand and interpret.',
+        variable: {
+          isRequired: true,
+          allowedTypes: ['number'],
+          hasMultiple: false,
+        },
+        coVariable: {
+          isRequired: true,
+          allowedTypes: ['number'],
+          hasMultiple: true,
+        },
+      },
+      {
+        id: 'logistic-regression',
+        label: 'Logistic Regression',
+        description:
+          'Logistic regression is a statistical method for predicting the probability of a binary event.',
+        variable: {
+          isRequired: true,
+          allowedTypes: ['nominal'],
+          hasMultiple: false,
+          hint: 'A binary event to predict',
+        },
+        coVariable: {
+          isRequired: true,
+          allowedTypes: ['number'],
+          hasMultiple: true,
+        },
+        parameters: [
+          {
+            name: 'pos-level',
+            label: 'Positive level',
+            linkedTo: AllowedLink.VARIABLE,
+            isRequired: true,
+          },
+          {
+            name: 'neg-level',
+            label: 'Negative level',
+            linkedTo: AllowedLink.VARIABLE,
+            isRequired: true,
+          },
+        ],
+      },
+    ];
   }
 
   async getHistogram(
-    variable: string,
+    variable: Variable,
     datasets: string[],
     cookie?: string,
   ): Promise<RawResult> {
     const url = new URL(this.options.baseurl + `histogram`);
 
-    url.searchParams.append('var', variable);
+    url.searchParams.append('var', variable.id);
     url.searchParams.append('type', 'combine');
     url.searchParams.append('cohorts', datasets.join(','));
 
@@ -114,10 +168,20 @@ export default class DataShieldConnector implements Connector {
       };
     }
 
-    const title = variable.replace(/\./g, ' ').trim();
+    const title = variable.label ?? variable.id;
     const data = { ...response.data, title };
 
-    const chart = transformToHisto.evaluate(data);
+    if (variable.type === 'nominal' && variable.enumerations) {
+      data['lookup'] = variable.enumerations.reduce((prev, curr) => {
+        prev[curr.value] = curr.label;
+        return prev;
+      }, {});
+    }
+
+    const chart =
+      variable.type === 'nominal'
+        ? transformToHistoNominal.evaluate(data)
+        : transformToHisto.evaluate(data);
 
     return {
       rawdata: {
@@ -128,13 +192,13 @@ export default class DataShieldConnector implements Connector {
   }
 
   async getDescriptiveStats(
-    variable: string,
+    variable: Variable,
     datasets: string[],
     cookie?: string,
   ): Promise<TableResult> {
     const url = new URL(this.options.baseurl + 'quantiles');
 
-    url.searchParams.append('var', variable);
+    url.searchParams.append('var', variable.id);
     url.searchParams.append('type', 'split');
     url.searchParams.append('cohorts', datasets.join(','));
 
@@ -148,9 +212,35 @@ export default class DataShieldConnector implements Connector {
       }),
     );
 
-    const title = variable.replace(/\./g, ' ').trim();
+    const title = variable.label ?? variable.id;
     const data = { ...response.data, title };
-    const table = transformToTable.evaluate(data);
+
+    const table = (
+      variable.enumerations
+        ? transformToTableNominal.evaluate(data)
+        : transformToTable.evaluate(data)
+    ) as TableResult;
+
+    if (
+      table &&
+      table.headers &&
+      variable.type === 'nominal' &&
+      variable.enumerations
+    ) {
+      table.headers = table.headers.map((header) => {
+        const category = variable.enumerations.find(
+          (v) => v.value === header.name,
+        );
+
+        if (!category || !category.label) return header;
+
+        return {
+          ...header,
+          name: category.label,
+        };
+      });
+    }
+
     return {
       ...table,
       tableStyle: TableStyle.DEFAULT,
@@ -168,6 +258,11 @@ export default class DataShieldConnector implements Connector {
     const expResult: Experiment = {
       id: `${data.algorithm.id}-${Date.now()}`,
       variables: data.variables,
+      coVariables: data.coVariables,
+      author: {
+        username: user.username,
+        fullname: user.fullname ?? user.username,
+      },
       name: data.name,
       domain: data.domain,
       datasets: data.datasets,
@@ -176,21 +271,37 @@ export default class DataShieldConnector implements Connector {
       },
     };
 
+    const allVariablesId = [...data.variables, ...data.coVariables];
+
+    const allVariables = await this.engineService.getVariables(
+      expResult.domain,
+      allVariablesId,
+      request,
+    );
+
     switch (data.algorithm.id) {
       case 'MULTIPLE_HISTOGRAMS': {
         expResult.results = await Promise.all<RawResult>(
-          data.variables.map((variable) =>
+          allVariables.map((variable) =>
             this.getHistogram(variable, expResult.datasets, cookie),
           ),
         );
         break;
       }
       case 'DESCRIPTIVE_STATS': {
-        expResult.results = await Promise.all<TableResult>(
-          [...data.variables, ...data.coVariables].map((variable) =>
-            this.getDescriptiveStats(variable, expResult.datasets, cookie),
-          ),
-        );
+        // Cannot be done in parallel because Datashield API has an issue with parallel request (response mismatching)
+        const results = [];
+        for (const variable of allVariables) {
+          const result = await this.getDescriptiveStats(
+            variable,
+            expResult.datasets,
+            cookie,
+          );
+
+          results.push(result);
+        }
+
+        expResult.results = results;
         break;
       }
     }

api/src/engine/connectors/datashield/transformations.ts

@@ -30,6 +30,38 @@ export const transformToDomain = jsonata(`
 }
 `);
 
+export const transfoToHistoNominal = jsonata(`
+(
+  {
+  "chart": {
+    "type": 'column'
+  },
+  "legend": {
+    "enabled": false
+  },
+  "series": [{
+      "name": "Count",
+      "data": global.*   
+  }],
+  "title": {
+    "text": title ? title : ''
+  },
+  "tooltip": {
+    "enabled": true
+  },
+  "xAxis": {
+    "categories": $keys(global).(
+      $param := $lookup($$.lookup, $);
+      $param ? $param : $
+    )
+  },
+  "yAxis": {
+    "min": 0,
+    "minRange": 0.1,
+    "allowDecimals": true
+  }
+})`);
+
 export const transformToHisto = jsonata(`
 (
   $nbBreaks := $count(global.breaks);
@@ -74,6 +106,21 @@ export const transformToTable = jsonata(`
       "name": $,
       "type": "string"
   },
+  "data": $.$each(function($v, $k) {
+         $not($k in $params) ? $append($k,$v) : undefined
+      })[]
+})
+`);
+
+export const transformToTableNominal = jsonata(`
+(
+  $params := ["title"];
+  {
+  "name": "Descriptive Statistics",
+  "headers": $append(title, $keys($.*)).{
+      "name": $,
+      "type": "string"
+  },
   "data": $.$each(function($v, $k) {
          $not($k in $params) ? $append($k,$v.*) : undefined
       })[]

api/src/engine/engine.service.ts

@@ -29,6 +29,7 @@ import {
 import { ListExperiments } from './models/experiment/list-experiments.model';
 import { FilterConfiguration } from './models/filter/filter-configuration';
 import { FormulaOperation } from './models/formula/formula-operation.model';
+import { Variable } from './models/variable.model';
 
 /**
  * Engine service.
@@ -46,7 +47,7 @@ export default class EngineService implements Connector {
   ) {
     import(`./connectors/${options.type}/${options.type}.connector`).then(
       (conn) => {
-        const instance = new conn.default(options, httpService);
+        const instance = new conn.default(options, httpService, this);
 
         if (instance.createExperiment && instance.runExperiment)
           throw new InternalServerErrorException(
@@ -96,7 +97,7 @@ export default class EngineService implements Connector {
 
     const result = await fn();
 
-    this.cacheManager.set(key, result);
+    this.cacheManager.set(key, result, { ttl: this.cacheConf.ttl });
 
     return result;
   }
@@ -118,6 +119,29 @@ export default class EngineService implements Connector {
     );
   }
 
+  /**
+   * It takes a domain ID and a list of variable IDs, and returns a list of variables that match the IDs
+   * @param {string} domainId - The domain ID of the domain you want to get variables from.
+   * @param {string[]} varIds - The list of variable IDs to get.
+   * @param {Request} request - The request object from the HTTP request.
+   * @returns An array of variables
+   */
+  async getVariables(
+    domainId: string,
+    varIds: string[],
+    request: Request,
+  ): Promise<Variable[]> {
+    if (!domainId || varIds.length === 0) return [];
+
+    const domains = await this.getDomains([], request);
+
+    return (
+      domains
+        .find((d) => d.id === domainId)
+        ?.variables?.filter((v) => varIds.includes(v.id)) ?? []
+    );
+  }
+
   async createExperiment(
     data: ExperimentCreateInput,
     isTransient: boolean,

api/src/engine/models/experiment/algorithm.model.ts

 import { Field, ObjectType } from '@nestjs/graphql';
 import { BaseParameter } from './algorithm/base-parameter.model';
+import { NominalParameter } from './algorithm/nominal-parameter.model';
+import { NumberParameter } from './algorithm/number-parameter.model';
 import { VariableParameter } from './algorithm/variable-parameter.model';
 
+type Parameter = BaseParameter | NumberParameter | NominalParameter;
+
 @ObjectType()
 export class Algorithm {
   @Field()
   id: string;
 
   @Field(() => [BaseParameter], { nullable: true, defaultValue: [] })
-  parameters?: BaseParameter[];
+  parameters?: Parameter[];
 
   @Field(() => VariableParameter)
   variable?: VariableParameter;

api/src/engine/models/experiment/algorithm/nominal-parameter.model.ts

 import { Field, ObjectType, registerEnumType } from '@nestjs/graphql';
 import { BaseParameter } from './base-parameter.model';
 
-enum AllowedLink {
+export enum AllowedLink {
   VARIABLE = 'VARIABLE',
   COVARIABLE = 'COVARIABLE',
 }

api/src/engine/models/experiment/algorithm/variable-parameter.model.ts

@@ -6,11 +6,14 @@ export class VariableParameter {
   hint?: string;
 
   @Field({ nullable: true, defaultValue: false })
-  isRequired: boolean;
+  isRequired?: boolean;
 
   @Field({ nullable: true, defaultValue: false })
-  hasMultiple: boolean;
+  hasMultiple?: boolean;
 
-  @Field(() => [String], { nullable: true })
-  allowedTypes: string[];
+  @Field(() => [String], {
+    nullable: true,
+    description: 'If undefined, all types are allowed',
+  })
+  allowedTypes?: string[];
 }

api/src/schema.gql

@@ -147,6 +147,8 @@ type VariableParameter {
   hint: String
   isRequired: Boolean
   hasMultiple: Boolean
+
+  """If undefined, all types are allowed"""
   allowedTypes: [String!]
 }